Deconvolution switch Bug in deconvolution.bsh

spim_registration/timelapse/deconvolution_GPU.bsh → spim_registration/timelapse/deconvolution.bsh

@@ -4,11 +4,11 @@ import ij.Prefs; 	// calls imagej settings
 import java.lang.Runtime;
 import java.io.File;
 import java.io.FilenameFilter;
- 
+
 runtime = Runtime.getRuntime();
 System.out.println(runtime.availableProcessors() + " cores available for multi-threading");
 
-Prefs.setThreads(7); 	// defines the number of threads allowed 
+Prefs.setThreads(7); 	// defines the number of threads allowed
 print("Threads: "+Prefs.getThreads()); // prints thread setting in output
 
 System.out.println( "Start to load Parameters:" );
@@ -27,13 +27,12 @@ int parallel_timepoints = Integer.parseInt(System.getProperty( "parallel_timepoi
 process_timepoint = System.getProperty( "process_timepoint" );
 process_channel = System.getProperty( "process_channel" );
 process_illumination = System.getProperty( "process_illumination" );
-process_angle = System.getProperty( "process_angle" ); 
-
+process_angle = System.getProperty( "process_angle" );
 
 System.out.println( "-------------------------------------------------------" );
 System.out.println( "General parameters: " );
 System.out.println( "timepoint_processed = " + parallel_timepoints );
-System.out.println( "process_timepoints = " + process_timepoint ); 
+System.out.println( "process_timepoints = " + process_timepoint );
 System.out.println( "process_channel = " + process_channel );
 System.out.println( "process_illumination = " + process_illumination );
 System.out.println( "process_angle = " + process_angle );
@@ -66,7 +65,6 @@ psf_estimation = System.getProperty( "psf_estimation" );
 iterations = System.getProperty( "iterations" );
 deco_output_file_directory = System.getProperty( "deco_output_file_directory" );
 
-
 System.out.println( "-------------------------------------------------------" );
 System.out.println( "Deconvolution settings: " );
 System.out.println( "imglib2_container = " + imglib2_container_deco );
@@ -95,24 +93,24 @@ System.out.println( "-------------------------------------------------------" );
 System.out.println( "Channel Settings: " );
 // Channel setting for Deconvolution
 // parses channels and takes from there the number of channels
-// parses detections_to_extract_psf_for_channel 
+// parses detections_to_extract_psf_for_channel
 channels = System.getProperty( "channels" );
-System.out.println( "Channels = " + channels ); 
+System.out.println( "Channels = " + channels );
 
 detections_to_extract_psf_for_channel = System.getProperty( "detections_to_extract_psf_for_channel" );
 System.out.println( "PSF: " + detections_to_extract_psf_for_channel );
 
-// Splits channels and detections_to_extract_psf_for_channel 
+// Splits channels and detections_to_extract_psf_for_channel
 String delims = "[,]";
 String[] channel_token = channels.split(delims);
 String[] psf_token = detections_to_extract_psf_for_channel.split(delims);
-		
-// Assembles channel_string 
+
+// Assembles channel_string
 StringBuilder channel_string = new StringBuilder();
 
 for (int channel=0; channel < channel_token.length; channel++ )
 
-{	
+{
 	String channel_part = "detections_to_extract_psf_for_channel_" + channel_token[channel] + "=" + psf_token[channel] + " ";
 	channel_string.append( channel_part );
 	channel_string.append(" ");
@@ -131,20 +129,20 @@ System.getProperty( "cudafourierconvolution = " + cudafourierconvolution );
 System.out.println( "compute_on = " + compute_on );
 System.out.println( "directory_cuda = " + directory_cuda  );
 System.out.println( "cudafourierconvolution = " + cudafourierconvolution );
-	
+
 String compute_string = "";
 String cuda_settings = "";
-		
+
 if (compute_on.equalsIgnoreCase( "GPU (Nvidia CUDA via JNA)" ) )
 {
 	System.out.println( "GPU deconvoultion selected" );
 	compute_string = "compute_on=[GPU (Nvidia CUDA via JNA)] ";
 	cuda_settings = "cuda_directory=" + directory_cuda + " " +
-			"select_native_library_for_cudafourierconvolution=" + cudafourierconvolution + " " + 
+			"select_native_library_for_cudafourierconvolution=" + cudafourierconvolution + " " +
 			"gpu_1 ";
 }
-		
-else if (compute_on.equalsIgnoreCase( "CPU (Java)" ) ) 
+
+else if (compute_on.equalsIgnoreCase( "CPU (Java)" ) )
 {
 	System.out.println( "CPU deconvoultion selected" );
 	compute_string = "compute_on=[" + compute_on + "] ";

spim_registration/timelapse/tomancak_test_cluster.yaml

@@ -149,7 +149,7 @@ deconvolution: {
   maximal_x_deco: '1019', # essential maybe automate
   maximal_y_deco: '1941', # essential maybe automate
   maximal_z_deco: '486', # essential maybe automate
-  detections_to_extract_psf_for_channel: '"beads"',
+  detections_to_extract_psf_for_channel: '"beads,beads"',
   process_timepoint: '"Single Timepoint (Select from List)"',
   process_angle: '"All angles"',
   process_channel: '"All channels"',
@@ -165,7 +165,7 @@ deconvolution: {
   psf_size_y: '19',
   psf_size_z: '25',
   type_of_iteration: '"Efficient Bayesian - Optimization I (fast, precise)"',
-  bsh_file: "deconvolution_GPU.bsh"
+  bsh_file: "deconvolution.bsh"
   }
   
 hdf5_output: {